Automatic target recognition (ATR) is an important part for many computer vision applications. Despite the extensive research which has been carried out in this area for many years, there is no ATR system which performs well on all applications. Recently, different object recognition frameworks have been proposed which yield a high performance in baseline databases. However, our experiments showed that they can fail in real-world scenarios, when dealing with a limited number of data samples. In this paper, we propose a new ATR system, based on deep convolutional neural network (DCNN), to detect the targets in forward looking infrared (FLIR) scenes and recognize their classes. In our proposed ATR framework, a fully convolutional network is trained to map the input FLIR imagery data to a fixed stride correspondingly-sized target score map. The potential targets are identified by applying a threshold on the target score map. Finally, the corresponding regions centered at these target points are fed to a DCNN to classify them into different target types while at the same time rejecting the false alarms. The proposed architecture achieves a significantly better performance in comparison with that of the state-of-the-art methods on two large FLIR image databases.